MetaQC

Package: MetaQC
Type: Package
Title: MetaQC: Objective Quality Control and Inclusion/Exclusion
Criteria for Genomic Meta-Analysis
Version: 0.1.13
Author: Don Kang <donkang75@gmail.com> and George Tseng
<ctseng@pitt.edu>
Maintainer: Don Kang <donkang75@gmail.com>
Description: MetaQC implements our proposed quantitative quality
control measures: (1) internal homogeneity of co-expression
structure among studies (internal quality control; IQC); (2)
external consistency of co-expression structure correlating
with pathway database (external quality control; EQC); (3)
accuracy of differentially expressed gene detection (accuracy
quality control; AQCg) or pathway identification (AQCp); (4)
consistency of differential expression ranking in genes
(consistency quality control; CQCg) or pathways (CQCp). (See
the reference for detailed explanation.) For each quality
control index, the p-values from statistical hypothesis testing
are minus log transformed and PCA biplots were applied to
assist visualization and decision. Results generate systematic
suggestions to exclude problematic studies in microarray
meta-analysis and potentially can be extended to GWAS or other
types of genomic meta-analysis. The identified problematic
studies can be scrutinized to identify technical and biological
causes (e.g. sample size, platform, tissue collection,
preprocessing etc) of their bad quality or irreproducibility
for final inclusion/exclusion decision.
Depends: R (>= 2.10.0), proto, foreach, iterators
Suggests: doMC, doSNOW, FactoMineR, matrixStats, gdata, gtools,
survival
License: GPL-2
URL: https://github.com/donkang75/MetaQC
LazyLoad: yes
Collate: MetaQC.R requireAll.R functions.R runQC.R cleanup.R
Date: 2012-12-21
Packaged: 2012-12-21 22:10:50 UTC; ddkang
Repository: CRAN
Date/Publication: 2012-12-22 07:39:42

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MetaQC' ...
** package 'MetaQC' successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MetaQC'
    finding HTML links ... done
    MetaQC-package                          html  
    MetaQC                                  html  
    brain                                   html  
    cleanup                                 html  
    plot.proto                              html  
    print.proto                             html  
    requireAll                              html  
    runQC                                   html  
** building package indices
** testing if installed package can be loaded
* DONE (MetaQC)
Making 'packages.html' ... done